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Kim Y, Lee D, Kim J. Effects of incubation temperature and acetonitrile amount on microwave-assisted tryptic digestion of proteins. Anal Biochem 2019; 569:31-38. [PMID: 30707897 DOI: 10.1016/j.ab.2019.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 11/29/2022]
Abstract
The effects of incubation temperature and acetonitrile (ACN) amount on microwave-assisted tryptic digestion of horse skeletal muscle myoglobin (MYG) and bovine serum albumin (BSA) were investigated. Microwave-assisted tryptic digestion was performed on BSA or MYG solutions containing different amounts (0, 10, and 20%) of ACN for different times (10, 20, 30, 40, and 50 min) at different temperatures (25, 37, and 55 °C). Conventional overnight tryptic digestion was also conducted with gentle mixing at 37 °C for 16 h. Digested samples were analyzed using matrix-assisted laser desorption/ionization mass spectrometry. Similar sequence coverage (SC) values were obtained under most conditions except when the protein sample solutions were digested with 20% ACN at 55 °C, which provided the lowest SC for both MYG and BSA for all investigated digestion times. Considering the missed cleavage (MC) ratios for 50-min microwave-assisted digestion, the highest MC ratio, (i.e., lowest trypsin activity) was observed for the digestion condition of 20% ACN at 55 °C for both proteins, while the lowest MC ratio was observed with 0% ACN at 25 °C for MYG and with 0% ACN at 55 °C for BSA. Conventional overnight tryptic digestion at 37 °C provided more completely cleaved peptides than 50-min microwave-assisted tryptic digestion at the same temperature.
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Affiliation(s)
- Yeoseon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Dabin Lee
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea.
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Shin D, Lee D, Kim Y, Kim I, Paek J, Kim J. Comparison of freeze vacuum drying and conventional drying methods in matrix-assisted laser desorption/ionization mass spectrometry analyses of peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1746-1750. [PMID: 29971856 DOI: 10.1002/rcm.8225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/23/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Dongwon Shin
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Dabin Lee
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Yeoseon Kim
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Inyoung Kim
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jihyun Paek
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
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Srzentić K, Zhurov KO, Lobas AA, Nikitin G, Fornelli L, Gorshkov MV, Tsybin YO. Chemical-Mediated Digestion: An Alternative Realm for Middle-down Proteomics? J Proteome Res 2018; 17:2005-2016. [PMID: 29722266 DOI: 10.1021/acs.jproteome.7b00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein digestion in mass spectrometry (MS)-based bottom-up proteomics targets mainly lysine and arginine residues, yielding primarily 0.6-3 kDa peptides for the proteomes of organisms of all major kingdoms. Recent advances in MS technology enable analysis of complex mixtures of increasingly longer (>3 kDa) peptides in a high-throughput manner supporting the development of a middle-down proteomics (MDP) approach. Generating longer peptides is a paramount step in launching an MDP pipeline, but the quest for the selection of a cleaving agent that would provide the desired 3-15 kDa peptides remains open. Recent bioinformatics studies have shown that cleavage at the rarely occurring amino acid residues such as methionine (Met), tryptophan (Trp), or cysteine (Cys) would be suitable for MDP approach. Interestingly, chemical-mediated proteolytic cleavages uniquely allow targeting these rare amino acids, for which no specific proteolytic enzymes are known. Herein, as potential candidates for MDP-grade proteolysis, we have investigated the performance of chemical agents previously reported to target primarily Met, Trp, and Cys residues: CNBr, BNPS-Skatole (3-bromo-3-methyl-2-(2-nitrophenyl)sulfanylindole), and NTCB (2-nitro-5-thiobenzoic acid), respectively. Figures of merit such as digestion reproducibility, peptide size distribution, and occurrence of side reactions are discussed. The NTCB-based MDP workflow has demonstrated particularly attractive performance, and NTCB is put forward here as a potential cleaving agent for further MDP development.
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Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | | | - Anna A Lobas
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia
| | - Gennady Nikitin
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015 , Switzerland
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics , Russian Academy of Sciences , Leninsky Prospect 38 , Moscow 119334 , Russia.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. , Dolgoprudny, Moscow 141707 , Russia
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park , Lausanne 1015 , Switzerland
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Shin D, Kim I, Paek J, Kim J. A Novel “Freeze Vacuum Drying” Crystallization Method Toward Quantitative MALDI-MS. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Dongwon Shin
- Department of Chemistry; Chungnam National University; Daejeon 305-764 Republic of Korea
| | - Inyoung Kim
- Department of Chemistry; Chungnam National University; Daejeon 305-764 Republic of Korea
| | - Jihyun Paek
- Department of Chemistry; Chungnam National University; Daejeon 305-764 Republic of Korea
| | - Jeongkwon Kim
- Department of Chemistry; Chungnam National University; Daejeon 305-764 Republic of Korea
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Laskay ÜA, Srzentić K, Monod M, Tsybin YO. Extended bottom-up proteomics with secreted aspartic protease Sap9. J Proteomics 2014; 110:20-31. [DOI: 10.1016/j.jprot.2014.07.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/04/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
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Optimization of separation and digestion conditions in immune complexome analysis. Anal Biochem 2013; 443:181-6. [DOI: 10.1016/j.ab.2013.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022]
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Park S, Kim T, Lee J, Seo M, Kim J. Effect of phosphoric acid as a matrix additive in matrix-assisted laser desorption/ionization analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:842-846. [PMID: 23495031 DOI: 10.1002/rcm.6508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 01/10/2013] [Accepted: 01/13/2013] [Indexed: 06/01/2023]
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Shin S, Yang HJ, Kim JH, Kim J, Lee JH, Park KH, Kim HS, Kim J. Clarification of a peak at m/z 1634 from tryptically digested cytochrome c. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1576-1581. [PMID: 23280746 DOI: 10.1002/jms.3119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/03/2012] [Accepted: 10/04/2012] [Indexed: 06/01/2023]
Abstract
A peptide peak at m/z 1634 in the mass spectrum of tryptically digested cytochrome c has been ambiguously assigned to either a peptide IFVQKCAQCHTVEK or a peptide CAQCHTVEK combined with a heme group (CAQCHTVEK + heme (Fe(III))). A comprehensive investigation was performed to clearly identify the origin of the peak. Tryptic digests of cytochrome c were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), liquid chromatography-tandem MS (LC-MS/MS), LC-ultraviolet (LC-UV), and MALDI Fourier transform-ion cyclotron resonance (FT-ICR) MS. The use of instruments with extremely high mass accuracy revealed the mass difference between the IFVQKCAQCHTVEK and the (CAQCHTVEK + heme (Fe(III))) ions. Fragmentation of the peptide associated with the unknown peak yielded a heme ion and other fragment ions originating from a (CAQCHTVEK + heme (Fe(III))) ion. Furthermore, an absorption peak at 395 nm confirmed the presence of a heme group in the unknown peptide. High mass accuracy analyses of MS and MS/MS spectra, in addition to three-dimensional UV contour mapping, showed that the peak at m/z 1634 is due to a (CAQCHTVEK + heme (Fe(III))) ion and not from protonated IFVQKCAQCHTVEK.
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Zhou H, Ning Z, E. Starr A, Abu-Farha M, Figeys D. Advancements in Top-Down Proteomics. Anal Chem 2011; 84:720-34. [DOI: 10.1021/ac202882y] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Zhibing Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
| | - Mohamed Abu-Farha
- Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5
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